GEO help: Mouse over screen elements for information.
Status
Public on Oct 25, 2012
Title
08257T1
Sample type
genomic
Source name
08257T1
Organism
Homo sapiens Characteristics
tissue: Normal
Extracted molecule
genomic DNA
Extraction protocol
Acquired from Tissue Solutions Ltd
Label
Biotin
Label protocol
As per manufacturer (Affymetrix)
Hybridization protocol
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description
EA09054_0711-01B_GenomeWideSNP_6_08257T1.birdseed-v2.chp
Data processing
CEL files were generated with GCOS, and further processed using default algorithms for normalization and genotype calling in Affymetrix Genotyping Consol.
Submission date
Jun 15, 2011
Last update date
Oct 25, 2012
Contact name
Joanna Dawn Holbrook
E-mail(s)
Joanna_Holbrook@sics.a-star.edu.sg Organization name
Singapore Institute of Clinical Sciences
Street address
30 Medical Drive
City
Singapore
ZIP/Postal code
117609
Country
Singapore
Platform ID
GPL6801 Series (2)
GSE29996 Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Affymetrix SNP array data]
GSE29999 Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine
Data table header descriptions ID_REF VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
Confidence strengh of the call (smaller is better)
Signal A Summarized signal for allele A
Signal B Summarized signal for allele B
Data table ID_REF VALUE Confidence Signal A Signal B SNP_A-2131660
BB
0.005
690.867
2825.887
SNP_A-1967418
BB
0.002
260.155
750.007
SNP_A-1969580
BB
0.005
1114.069
3545.433
SNP_A-4263484
AB
0.005
1823.215
1466.890
SNP_A-1978185
AA
0.004
1793.288
379.062
SNP_A-4264431
AB
0.001
1006.401
755.724
SNP_A-1980898
BB
0.008
295.739
1120.468
SNP_A-1983139
AA
0.006
2280.231
586.710
SNP_A-4265735
AA
0.004
1016.625
388.632
SNP_A-1995832
AB
0.004
1495.630
1134.492
SNP_A-1995893
AB
0.003
1279.473
1390.287
SNP_A-1997689
BB
0.008
744.087
3450.867
SNP_A-1997709
AA
0.013
2059.744
284.019
SNP_A-1997896
AB
0.004
947.435
1633.088
SNP_A-1997922
AA
0.002
872.993
285.796
SNP_A-2000230
AA
0.008
2647.955
982.197
SNP_A-2000332
AA
0.004
2722.888
899.969
SNP_A-2000337
AA
0.000
1841.229
340.392
SNP_A-2000342
AA
0.003
2824.064
790.030
SNP_A-4268173
AA
0.001
1231.144
259.559
909622 35506 Kbytes .Supplementary file Size Download File type/resource GSM742390.CEL.gz
34.2 Mb
(ftp) (http) CEL
GSM742390.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
